Tomorrow Apple will release it's version 10.11 of OSX called "El Capitan".
Although not a whole lot is changing on the outside, there is one big (and often unreported) change that will affect 'power users' like bioinformaticians, and that's the introduction of "System Integrity Protection" or SIP. Although it doesn't remove the root account per se, it will prevent all users (including root) from modifying or writing to system paths and files. These paths include:
- /usr (except /usr/local)
Any files not part of Apple's core system will be moved out of these locations, although i'm currently not sure where too (probably /usr/local).
Any hardcoded paths or software you have installed in these system paths will obviously cease to work.
Also, any tools not cryptographically signed by Apple via the AppStore (which is pretty much all bioinformatic software for OSX) will no longer be able to interact in certain low-level ways with the kernel. For example, any scripts you use that make use of DTrace (Apple-made like iosnoop, or 3rd party like the workflow logger i just upgraded to make use of DTrace -_-; ) will no longer work. Apparently this only affects "restricted processes" but from what i've tested this seems to be everything. I have no idea which bioinformatic software, if any, use such low-level interaction with the OSX kernel, but certainly the following applications you might currently be using will no longer work:
- TotalTerminal, TotalFinder and TotalSpaces
- SuperDuper (restored backups will have SIP turned off)
- lldb (popular debugger that ships with OSX now can only attach to non-protected processes)
- A whole bunch of python modules (eg. lxml)
Also, unrelated to System Integrity Protection, anyone using a non-Apple SSD may remember that Yosemite prevented TRIM support by 3rd party apps. TRIM makes your SSD last a lot longer, and perform about 5x faster. It's now back in El Capitan, as a program called Trimforce, but you have to turn it on manually and accept the waiver that the SSD might become corrupt, although there's a pretty tiny chance that this will happen if its a new TRIM-compatible SSD.
I am hoping that in the next few days we WONT see a huge number of complaints about xyz software no longer working, but to be on the safe-side I suggest sticking to OSX 10.10 until you know your pipeline will work on 10.11 :)